biolink/biolink-model issues and pull requests

#1313 - Infores as YAML instead of TSV to avoid formatting issues

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1312 - make document type slot multivalued

Pull Request - State: closed - Opened by vincentvialard over 1 year ago

#1311 - deprecated entities still referenced in the model itself

Issue - State: open - Opened by vincentvialard over 1 year ago
Labels: bug

#1310 - infores catalog: add BioThings RARe-SOURCE API and NCATS RARe-SOURCE

Pull Request - State: closed - Opened by colleenXu over 1 year ago - 3 comments

#1309 - revised property in collaboration with Casey Ta

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1308 - deprecating sources via conversation in slack about biggim, bigclam, and clinical-profiles, also fixes #1291

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1307 - Propose definition for biolink:population_count

Pull Request - State: closed - Opened by CaseyTa over 1 year ago

#1306 - infores catalog - some rows missing columns, causing bmt to crash

Issue - State: closed - Opened by CaseyTa over 1 year ago - 3 comments

#1305 - Add code to check that URLs in infores data dictionary resolve

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1304 - Update infores format, fix broken rows, add inforeses for monarchinitiative

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1303 - updates for automat infores entries

Pull Request - State: closed - Opened by EvanDietzMorris over 1 year ago

#1302 - Formatting issue in infores_catalog_nodes rendering

Issue - State: closed - Opened by nlharris over 1 year ago - 1 comment
Labels: documentation

#1301 - Add new clinical edge attributes to model

Issue - State: open - Opened by karafecho over 1 year ago - 6 comments
Labels: working-group/clinical

#1300 - update doc links, copy biolink-model.yaml into the docs dir, copy predicate map into docs dir.

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1299 - Some broken links on the Github.io pages for browsing the BIolink Model

Issue - State: closed - Opened by justaddcoffee over 1 year ago - 3 comments
Labels: documentation

#1298 - refactor catalyzes domain/range, fixes #1262

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1297 - fix prefix for biolink

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1297 - fix prefix for biolink

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1296 - fixes #1279 fixes #1216

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1295 - domain and range on "diagnoses" seem odd

Issue - State: closed - Opened by sierra-moxon over 1 year ago - 3 comments

#1294 - Semmeddb mappings per analysis in #1292, fixes #1295

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago - 1 comment

#1293 - Improved CAM-KP infores entries

Pull Request - State: closed - Opened by gaurav over 1 year ago

#1293 - Improved CAM-KP infores entries

Pull Request - State: closed - Opened by gaurav over 1 year ago

#1292 - generate domain/range validation report for SEMMEDDB

Issue - State: closed - Opened by sierra-moxon over 1 year ago - 4 comments
Labels: enhancement, help-desk

#1291 - Adding disease context qualifier to Biolink

Issue - State: closed - Opened by codewarrior2000 over 1 year ago - 3 comments
Labels: enhancement

#1290 - Update COHD URLs to Translator Wiki landing pages in Infores Catalog

Pull Request - State: closed - Opened by CaseyTa over 1 year ago

#1289 - Resolver for identifiers

Issue - State: closed - Opened by sooyounga over 1 year ago - 2 comments
Labels: enhancement, identifiers

#1288 - Add infores

Pull Request - State: closed - Opened by gloriachin over 1 year ago

#1288 - Add infores

Pull Request - State: closed - Opened by gloriachin over 1 year ago

#1287 - Poetry for artifacts

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1286 - Update codespell to ignore regenerated files

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1286 - Update codespell to ignore regenerated files

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1285 - codespell: configuration, github action + typos fixed

Pull Request - State: closed - Opened by yarikoptic over 1 year ago

#1284 - Setting URLs for Text Mining KPs

Pull Request - State: closed - Opened by edgargaticaCU over 1 year ago

#1284 - Setting URLs for Text Mining KPs

Pull Request - State: closed - Opened by edgargaticaCU over 1 year ago

#1283 - prepping for 3.2.8 release

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1282 - add a better description for xref

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1282 - add a better description for xref

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1281 - Added 4 missing URLs for Multiomics Provider KPs

Pull Request - State: closed - Opened by gglusman over 1 year ago

#1281 - Added 4 missing URLs for Multiomics Provider KPs

Pull Request - State: closed - Opened by gglusman over 1 year ago

#1280 - Add hpoa to infores catalog

Issue - State: closed - Opened by kevinschaper over 1 year ago - 4 comments
Labels: identifiers

#1280 - Add hpoa to infores catalog

Issue - State: closed - Opened by kevinschaper over 1 year ago - 4 comments
Labels: identifiers

#1279 - genetic_association not under associated with?

Issue - State: closed - Opened by cbizon over 1 year ago
Labels: bug, question

#1278 - How to import/use/extend biolink model in our schema

Issue - State: closed - Opened by sooyounga over 1 year ago - 2 comments
Labels: question

#1277 - Move mapping to RO 'results in movement of'

Pull Request - State: closed - Opened by balhoff over 1 year ago

#1277 - Move mapping to RO 'results in movement of'

Pull Request - State: closed - Opened by balhoff over 1 year ago

#1276 - Fix mappings and domains/ranges for inputs/outputs

Pull Request - State: closed - Opened by balhoff over 1 year ago

#1275 - Fix incorrect domains and ranges of 'actively involved in'/'actively involves'

Pull Request - State: closed - Opened by balhoff over 1 year ago

#1274 - Fix typo in 'colocalizes with' RO ID

Pull Request - State: closed - Opened by balhoff over 1 year ago

#1274 - Fix typo in 'colocalizes with' RO ID

Pull Request - State: closed - Opened by balhoff over 1 year ago

#1273 - Update infores_catalog_nodes.tsv

Pull Request - State: closed - Opened by karafecho over 1 year ago - 2 comments

#1272 - Add new infores:pgxmine to the catalog

Issue - State: open - Opened by codewarrior2000 over 1 year ago
Labels: enhancement, identifiers

#1272 - Add new infores:pgxmine to the catalog

Issue - State: open - Opened by codewarrior2000 over 1 year ago
Labels: enhancement, identifiers, working-group/MolePro

#1271 - fixes #1165 - refactors KEGG hardcoded prefixes and oboInOwl/oboformat/OIO prefix usage

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1270 - Add in_taxon_label as a node property

Pull Request - State: closed - Opened by kevinschaper over 1 year ago

#1270 - Add in_taxon_label as a node property

Pull Request - State: closed - Opened by kevinschaper over 1 year ago

#1269 - Remove singular, fixes #1268

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1268 - remove "singular_name" metadata from slots as it causes confusion with TRAPI

Issue - State: closed - Opened by sierra-moxon over 1 year ago - 2 comments

#1267 - fix according to Jim B's analysis, fixes #1257

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1267 - fix according to Jim B's analysis, fixes #1257

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1266 - minimum diff for infores url update

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1265 - update hpoa annotation url

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1264 - add space to yaml for better readability

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1263 - Update infores_catalog_nodes.tsv

Pull Request - State: closed - Opened by GitHubbit over 1 year ago

#1262 - Update/extend Publications model to support Publication Metadata API use cae

Issue - State: closed - Opened by mbrush over 1 year ago - 1 comment
Labels: enhancement

#1261 - Fix Wormbase ontology prefixes

Pull Request - State: closed - Opened by balhoff over 1 year ago - 3 comments

#1260 - add denormalized annotations for use in KGX

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1259 - Denormalized edge properties KGX SQL serialization

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1258 - Update infores_catalog_nodes.tsv

Pull Request - State: closed - Opened by karafecho over 1 year ago

#1257 - Wikidata prefix expansions in Biolink are for web pages, not entities

Issue - State: closed - Opened by balhoff over 1 year ago
Labels: bug, identifiers

#1256 - adding content for supporting publications modeling

Pull Request - State: closed - Opened by mbrush over 1 year ago - 1 comment

#1255 - Treats - for review for predicates

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1254 - add "support graphs" property to hold supporting statements of a creative mode query in TRAPI 1.4

Issue - State: closed - Opened by sierra-moxon over 1 year ago - 1 comment
Labels: enhancement

#1253 - add support graphs as a property of edges or nodes

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1252 - add slot usage required instead of broad slot required

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1251 - removing infores entries for automats that are no longer active

Pull Request - State: closed - Opened by EvanDietzMorris over 1 year ago

#1251 - removing infores entries for automats that are no longer active

Pull Request - State: closed - Opened by EvanDietzMorris over 1 year ago

#1250 - update smart api urls fixes #1245

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1246 - add infores for Richards Effector Gene List

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1246 - add infores for Richards Effector Gene List

Pull Request - State: closed - Opened by sierra-moxon over 1 year ago

#1245 - remove smartapi infores

Issue - State: closed - Opened by cbizon over 1 year ago - 4 comments
Labels: documentation

#1245 - remove smartapi infores

Issue - State: closed - Opened by cbizon over 1 year ago - 4 comments
Labels: documentation

#1239 - BioLink Model documentation does not give context to prefixes nor CURIEs

Issue - State: open - Opened by cthoyt over 1 year ago - 2 comments
Labels: documentation, identifiers

#1233 - added mpath mappings

Pull Request - State: closed - Opened by vincentvialard over 1 year ago

#1226 - Some biolink predicates no longer exist in latest Biolink Model

Issue - State: closed - Opened by nlharris almost 2 years ago - 4 comments
Labels: working-group/predicates

#1225 - add entity as a domain for id

Pull Request - State: closed - Opened by sierra-moxon almost 2 years ago

#1225 - add entity as a domain for id

Pull Request - State: closed - Opened by sierra-moxon almost 2 years ago

#1223 - should biolink:type (aka: rdf:type) be officially a node property?

Issue - State: closed - Opened by sierra-moxon almost 2 years ago
Labels: working-group/KGE

#1222 - adding classes from Ben H, fixes #1210

Pull Request - State: closed - Opened by sierra-moxon almost 2 years ago - 1 comment

#1221 - add domain to biolink:type to help KGX recognize it as a node property.

Pull Request - State: closed - Opened by sierra-moxon almost 2 years ago

#1221 - add domain to biolink:type to help KGX recognize it as a node property.

Pull Request - State: closed - Opened by sierra-moxon almost 2 years ago

#1219 - add grouping class for qualifiers, add subset translator, fix range o…

Pull Request - State: closed - Opened by sierra-moxon almost 2 years ago

#1217 - remove cycle in permissible values, fixes #1215, remove degradation from abundance hierarchy in permissible values, fixes #1206

Pull Request - State: closed - Opened by sierra-moxon almost 2 years ago

GitHub / biolink/biolink-model issues and pull requests